5ZVB | pdb_00005zvb

APOBEC3F Chimeric Catalytic Domain in Complex with DNA(dT9)

• PDB DOI: https://doi.org/10.2210/pdb5ZVB/pdb
• NAKB: 5ZVB

• Classification: STRUCTURAL PROTEIN/DNA
• Organism(s): Homo sapiens, DNA-binding vector pODB80
• Expression System: prokaryotic environmental samples
• Mutation(s): No 


• Deposited: 2018-05-09 Released: 2018-11-21 
• Deposition Author(s): Cheng, C., Zhang, T.L., Wang, C.X., Lan, W.X., Ding, J.P., Cao, C.Y.
• Funding Organization(s): National Science Foundation (China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.220 (Depositor), 0.217 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.173 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Literature

Crystal Structure of Cytidine Deaminase Human APOBEC3F Chimeric Catalytic Domain in Complex with DNA

Cheng, C., Zhang, T., Wang, C., Lan, W., Ding, J., Cao, C.

(2018) Chin J Chem 36: 1241-1248

• DOI: https://doi.org/10.1002/cjoc.201800508

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 53.42 kDa 
• Atom Count: 3,478 
• Modeled Residue Count: 374 
• Deposited Residue Count: 427 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
APEBEC3F/ssDNA-T9	A, B	209	Homo sapiens	Mutation(s): 0  Gene Names: APOBEC3G, MDS019, APOBEC3F EC: 3.5.4 (PDB Primary Data), 3.5.4.38 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IUX4 (Homo sapiens) Explore Q8IUX4  Go to UniProtKB:  Q8IUX4
PHAROS:  Q8IUX4 GTEx:  ENSG00000128394
Find proteins for Q9HC16 (Homo sapiens) Explore Q9HC16  Go to UniProtKB:  Q9HC16
PHAROS:  Q9HC16 GTEx:  ENSG00000239713
UniProt Groups	Q9HC16Q8IUX4

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*TP*TP*TP*TP*CP*AP*AP*T)-3')	C	9	DNA-binding vector pODB80

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CAC	E [auth A], G [auth B]	CACODYLATE ION C2 H6 As O2 OGGXGZAMXPVRFZ-UHFFFAOYSA-M
ZN	D [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.220 (Depositor), 0.217 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.173 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.99	α = 90
b = 92.702	β = 90
c = 93.674	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
ADDREF	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-11-21 
Deposition Author(s): Cheng, C., Zhang, T.L., Wang, C.X., Lan, W.X., Ding, J.P., Cao, C.Y.

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Funding Organization	Location	Grant Number
National Science Foundation (China)	China	91753119, 21778065 and 21472229

Revision History  

• Version 1.0: 2018-11-21
  Type: Initial release
  
• Version 1.1: 2018-11-28
  Changes: Data collection, Database references, Structure summary
• Version 1.2: 2024-10-23
  Changes: Data collection, Database references, Derived calculations, Structure summary